(738h) A Conformational Analysis of an Engineered Laminin-Mimetic, Elastin-like Fusion Protein Using Molecular Dynamics Simulations
AIChE Annual Meeting
2016
2016 AIChE Annual Meeting
Materials Engineering and Sciences Division
Modeling of Biomaterials
Thursday, November 17, 2016 - 5:21pm to 5:39pm
Methods: We adopted the crystal structure1DYK7 for the LG5 domain. The ELP[K2I2L2K2]1 sequence was built with the program Avogadro8 using the peptide builder tool. We assumed an alpha-helix starting structure with Φ = -60° and Ψ= -40° angles. Atomistic MD simulations were performed using NAMD 2.109 and the CHARMM36 force field for proteins. Temperatures were maintained using a Langevin thermostat. The production times for the simulations were 100 ns.
Results and Discussion: The first discrete event in protein folding within the elastin-like polypeptide (ELP) domain is the loss of the α-helix secondary structure and a transition to β type secondary structures. At temperatures below 305 K, we observed a collapse of the ELP domain with respect to its initial starting conformation. At 310 K, there is a noticeable transient unfolding of the ELP domain starting at ~75 ns, highlighted by the loss of intra-strand hydrogen bonds. The sudden appearance of intra- β-strands at 310 K also suggests an inverse phase transition at that temperature. This distinct folding transition to higher ordered structures has been shown to predict self-assembly in vitro observed by other groups10. Biomaterials incorporating this self-assembling property allow them to be highly dynamic, and can self-heal following external shear forces. An analysis into the hydration properties of the ELP domain reveals that as the temperature increases, the number of surrounding water molecules decreases and the number of peptide-peptide hydrogen bonds increases. There is a slight decrease in number of surrounding water molecules over time in all simulated temperatures, however, there is an abrupt reduction of water molecules at 64 ns and 82 ns at 310 K. This change in the hydration structure is correlated with the formation of β-sheets within the trajectory.
Conclusions: We introduce a realistic design strategy that could transform current approaches to biomaterials development and address the particular challenges of characterizing the dynamic processes that occur in biological matrices. Our simulations provide both an immediate, high-resolution view of the conformational dynamics of our system, as well as a robust and extensible platform for future work directed toward our overarching goal of creating self-assembling, protein-based biomaterials as candidates for cell-delivery therapeutics.
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